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Well, as the title suggests...I have only barely just stuck my toes into the ocean that is Anime...and I have made sure to try to view a "top-rated" anime from every genre, just to get a general idea of what I would or would not enjoy.

The one thing I really want to find is something that keeps you guessing, kind of a psychological thriller, or a horror one. I haven't ever seen anything like it...ideas?

Hmm, I can't say I concur with classifiying School Days as a psychological.... anything.

I'll definitely second Higurashi, Elfen Lied (not too psychological I think, but still an emotional and gruesome tour de force) and Madoka Magica, though. These fit the criteria very well, Higurashi in particular is exactly the kind of show where the mystery keeps you guessing. I'll warn you that Higurashi has a lot of tonal shifts throughout, bouncing back and forth between humorous and horror-focused episodes. If you can deal with that though, it's the cream of the crop.

There's really not too many choices when it comes to psychological horror in the anime medium. It's sadly a bit of a neglected genre. There's a lot of anime with violence that might be horrifying and intense, but the suspenseful and/or psychological element doesn't show up as often. Still, when pulling from the entirety of the medium, there's enough great stuff out there to keep you busy for a good while. Psychological horror happens to be my favorite genre, so I'll try to add a few recommendations from my vault of favorites.
Paranoia Agent. Satoshi Kon's excellent TV series. It doesn't get much more psychological than this. More creepy than actually scary (although it has its moments for sure), it is a psychological mystery which is both elegant and ingenious.
Boogiepop Phantom. Don't let the silly-sounding name fool you. This one is similarly themed, excelling mostly in mood. It has absolutely outstanding sound design, which enhances the dark atmosphere greatly.

Shiki. Unlike the previous two, this one is straight up psychological horror. And it is sublime. One of the best shows period of recent years, it breathes new life into a classic mythical creature, and tells it story with nigh-perfect pacing, characterization and horrifying scenes.

Jigoku Shoujo / Hell Girl An episodic series about a website from hell. Log on at midnight to have vengeance exacted upon the person who wronged you. The price? Your eternal soul. This one is contentious; people tend to love it or hate it. The stories have great mood, a depressing, almost misanthropic edge to them, and evoke a great sense of that classic Japanese-style horror.

Hope some of that will be of some use to you. Horror is a pretty subjective thing, so your mileage may of course vary from mine.

Another - I personally had some issues with the show but it is enjoyable and provides both suspense and horror elements and keeps you guessing. Threads were full of different theories at the time of airing.

Aoi Bungaku Series are a set of mini stories. They are not really horror but all of them have a hidden idea behind that makes you think. It's mostly drama though some stories do have horror elements.

Death Note, that's a given. Will be surprised if you haven't seen it already. It is all about mind games and keeps you guessing as to what will happen next. Main chara finds a notebook and whoever s name he writes in will die.

Elfen Lied - gory stuff with limbs getting cut off. As well as sad with some mind tricks.

Ga-Rei Zero is not horror but it is a bloody show with some interesting topics. Besides the way things are handled is very different from what I've seen in most action series. Really worth a watch.

Ghost Hunt - is one of my faves. You learn a lot of new stuff about ghost hunting. Series are separated in different arcs/cases. Some better than others. Labyrinth arc is my fave one. Though second arc will keep you at the edge as well

Highschool of the Dead - ZOMBIES! That alone says it all. One minus, too much fanservice.

Hundred Stories - has a very unique and different animation style what makes it feel much creepier than it would with normal style. Series are about Japanese legends and demons. Some episodes can be disturbing.

Jigoku Shoujo - are episodic series with mini story later on. Theme is very similar to Death Note, is it fine to kill bad people? Basically there is this girl who takes revenge for other people.

Mahou Shoujo Madoka★Magica - not a horror but psychological and full of twists and suspense. Cute art is very deceiving. Watched series in one go. Happens rarely for me.

Monster - not horros, detective series so suspense is there. A surgeon had once saved boy's life and years later learn that the boy has become into a serial killer. Surgeon feels responsible and tries to find him besides his accused of being a killer so he has to run and hide.

Phantom: Requiem for the Phantom - not a horror but suspense, drama, great soundtracks, interesting characters and great animation are included I personally adore this series.

Shiki - this series are slightly different. You as a viewer know who is the culprit but not the characters so you are stuck watching how village is fighting for their survival, every characters takes their own approach. Suspense included. Watched it one go too.

Steins;Gate - surprised that no one mentioned it considering it's popularity. Series are about time travelling and how tiny little changes in the past can change everything. Not a horror but second half will keep you at the edge of your seat.

First off let me say that Akira and Princess Mononoke are both must-see anime movies in the horror category (though neither of these is close to pure horror). Simply put, watch them if you haven't already.

Big seconds on Higurashi, Madoka, Steins;gate, School Days and Narutaru. Also, if you like Narutaru then you have to watch Bokurano which is by the same director. This one is pretty horrifying but on an almost entirely psychological level.

Of all of these Higurashi probably fits your criterion the best.

Another one that fits your criterion is the Kara no Kyoukai series. This one is almost ENTIRELY horror/suspense and is visually stunning. By that same token you might also enjoy Fate/Zero which is in large part actually a horror anime.

Some of my favorite oldschool Psychological Thrillers are Soultaker and Betterman. Soultaker is some of the craziest **** you'll ever watch, while Betterman is more of an under appreciated gem.

If you want something REALLY classic then check out Wicked City which was one of the most popular anime horror movies of the 80's. This one is over-the-top disturbing in almost every way.

You might also give Chrono Crusade and D. Gray-man a try but if you don't like action, the horror elements probably won't be enough to draw you in.

Also, Ergo Proxy is definitely suspense with a decent bit of horror. This show is like a big puzzle, in the same vein as Serial Experiments Lain, Boogiepop Phantom and Paranoia Agent

Haha I know what you mean. I didn't dare to watch Madoka at first either. Cute art with Magical girls was big push away. Then I heard about dark themes and was "Ok, let's see how dark it is. I bet it is... OMG! MORE!"

The first witch attack/animation is what made me go "Uuuuhhhh... nice!"

Since you saw Madoka I would recommend Steins;Gate as next since some themes are similar.

Most of the great ones have been recommended!
I'd like to throw in a few more that may qualify

Shikabane Hime Aka - a.k.a. Corpse Princess. These girls are living corpses, contracted to monks. Though the series heavily relies on action, it does have it's fair share of horror scenes.

xxxHoLiC - This should be classified more under psychological/supernatural as the protagonist can see spirits and works with a witch to fulfill wishes, though..not without paying a price. Some episodes were chilling because you never know what price the person has to pay.

Mouryou no Hako - Investigating the murders of schoolgirls who have been stuffed into boxes. Very dialogue-driven but leaves you thinking.